BIOL398-03/S13:Week 5

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==== ''Saccharomyces'' Genome Database ====
==== ''Saccharomyces'' Genome Database ====
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* Search for each of the genes encoding the enzymes in our metabolic pathway in the [http://www.yeastgenome.org ''Saccharomyces Genome Database'' (SGD)] and read their gene pages: 
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** ''GDH1''
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** ''GDH3''
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** ''GDH2''
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** ''GLN1''
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** ''GLT1''
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* Which of these genes has a homolog (similar gene related by descent) in humans?  What disease does a deficiency of this gene cause in humans?
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* How is the expression of each of these genes regulated?
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* Using the [http://pathway.yeastgenome.org/cpd-search.shtml compound search tool of SGD], search on "L-glutamate".  How many pathways does it participate in?
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* Find the SGD representation of the pathway we are working on in class and attach a screenshot and hyperlink to your journal page.  Choose the one that shows all of the reactions we talked about in class and make sure you can relate it to your notes, matching the genes, enzyme names, and reactants/products.
==== KEGG ====
==== KEGG ====

Revision as of 15:20, 12 February 2013

BIOL398-03: Biomathematical Modeling

MATH 388-01: Survey of Biomathematics

Loyola Marymount University

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NOTE: This page is still under construction.

This journal entry is due on Friday, February 15 at midnight PST (Thursday night/Friday morning). NOTE that the server records the time as Eastern Standard Time (EST). Therefore, midnight will register as 03:00.

Contents

Individual Journal Assignment

  • Store this journal entry as "username Week 5" (i.e., this is the text to place between the square brackets when you link to this page).
    • Create the following set of links. (HINT: you can do all of this easily by adding them to your template and then using the template on your pages.)
      • Link to your journal entry from your user page.
      • Link back from your journal entry to your user page.
      • Link to this assignment from your journal entry.
      • Don't forget to add the "BIOL398-03/S13" category to the end of your wiki page.

Exploring Pathway Databases

Explore the following pathway databases and answer the questions on your individual journal page. Illustrate your answers with screenshots and/or hyperlinks to database pages.

Saccharomyces Genome Database

  • Search for each of the genes encoding the enzymes in our metabolic pathway in the Saccharomyces Genome Database (SGD) and read their gene pages:
    • GDH1
    • GDH3
    • GDH2
    • GLN1
    • GLT1
  • Which of these genes has a homolog (similar gene related by descent) in humans? What disease does a deficiency of this gene cause in humans?
  • How is the expression of each of these genes regulated?
  • Using the compound search tool of SGD, search on "L-glutamate". How many pathways does it participate in?
  • Find the SGD representation of the pathway we are working on in class and attach a screenshot and hyperlink to your journal page. Choose the one that shows all of the reactions we talked about in class and make sure you can relate it to your notes, matching the genes, enzyme names, and reactants/products.

KEGG

Reactome

Shared Journal Assignment

  • Store your journal entry in the shared Class Journal Week 5 page. If this page does not exist yet, go ahead and create it (congratulations on getting in first :) )
  • Link to your journal entry from your user page.
  • Link back from the journal entry to your user page.
  • Sign your portion of the journal with the standard wiki signature shortcut (~~~~).
  • Add the "BIOL398-03/S13" category to the end of the wiki page (if someone has not already done so).

Reflection on Work

Read and Reflect

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